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<h1>Lab Notes - July</h1>
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<div id="page1">

<h1>Week1</h1>
<table id="notesheet" width="650" border="1" cellspacing="0"
	cellpadding="1" style="vertical-align: middle">
	<tr>
		<td width="76"><strong>Day</strong></td>
		<td width="349"><strong>Note</strong></td>
	</tr>

	<tr>
		<td id="sheetleft">Jul.4th Monday</td>
		<td>
		<table id="intable" width="328" border="0" cellspacing="0"
			cellpadding="1">

			<td width="128">• Aerobic cultivation of DH5α</td>


			<td width="196">• Preparation of apparatus for the formation of
			biofilm</td>

		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul 5th Tuesday</td>
		<td>&nbsp;</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.6th Wednesday</td>
		<td>
		<table width="217" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="215">•Receiving primers ordered previously</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.7th Thursday</td>
		<td>
		<table width="238" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="200">• Preparation of the aliquot of the primers</td>
				<td width="200">• Something wrong with a shaking incubator</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.8th Friday</td>
		<td>
		<table width="222" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="155">• Preparation of culture plates for the
				transformations</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.9th Saturday</td>
		<td>
		<table width="313" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="127">• Preparation of culture plates for the
				transformations</td>
				<td width="182">• protocols of transformation</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.10th Sunday</td>
		<td>
		<table width="246" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• Several colonies were picked up and cultivated in 5mL LB
				medium. •Cryosectioning of biofilm</td>
			</tr>
		</table>
		</td>
	</tr>

</table>
</p>
<h1>Week2</h1>
<table id="notesheet" width="650" border="1" cellspacing="0"
	cellpadding="1">
	<tr>
		<td width="76"><strong>Day</strong></td>
		<td width="349"><strong>Note</strong></td>
	</tr>

	<tr>
		<td id="sheetleft">Jul.11th Monday</td>
		<td>
		<table id="intable" width="541" border="0" cellspacing="0"
			cellpadding="1">

			<td width="128">• Set up new LB culture plates with ampicillin
			and kanamycin
			</p>
			</td>


			<td width="196">• ·Sterilization of Glycerol and <br />
			·Preparation of 25mg/mL kanamycin</td>
			<td>•Transformation of the parts mentioned on Jul.9th for the
			second time</td>
			<td>•Observation the sections</td>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul 12th Tuesday</td>
		<td>
		<table id="intable" width="560" border="0" cellspacing="0"
			cellpadding="1">

			<td width="128">• Pick two colonies of each parts and cultivate
			them in LB medium</td>


			<td width="203">•Transformation of three parts(20J,20H.22B from
			Kit plates of 2011 Distribution ) which are related to the
			degradation of Cellulose</td>
			<td width="91">•·Mini prep to isolate 10I,12I and 22M</td>
			<td width="130">•Conservation of 10I,12I,22M and 11P</td>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.13th Wednesday</td>
		<td>
		<table width="618" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="104">• Place the culture plate of 20J,20H and 22B in
				the fridge.</td>
				<td width="102">•Min prep to isolate 13K •Conservation of 13K</td>
				<td width="163">•Restriction digest of the
				parts(12I,10I,22M,13K) with EcoRI and PstI</td>
				<td width="111">•Gel electrophoresis to analyse restriction
				fragments</td>
				<td width="128">•Test the Tm of Primers CP1&amp;CS,NP&amp;NS
				with 13K. The result of Gel electrophoresis shows that 60.2℃ is the
				Tm of NS and NP, and 57.4℃ is the Tm of CS and CP1.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.14th Thursday</td>
		<td>
		<table width="618" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• Test the Tm of the YFP,RFP,tetR,Vgb and nirB primers.
				The result of Gel electrophoresis shows that the Tm for the primers
				of Vgb is 54℃ and the Tm for the primers of nirB is 55℃.The RCR of
				YFP,RFP and tetR failed.</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.15th Friday</td>
		<td>
		<table width="600" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="155">• PCR(Phusion)<br />
				• Digest 10I, 22M, 13K • Used wrong cutter, digestion again.</td>
				<td>• Run the results of PCR and the first digestion. The
				annealing temperature of YFP needed change. The digestion results
				confirmed</td>
				<td>• Run the digestion results of second time. The bands are
				confirmed.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.16th Saturday</td>
		<td>
		<table width="620" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="127">• Cut the linearized pSB1k3 with E+P</td>
				<td width="123">• Purify the digestion results of 22M, 13K, 10I</td>
				<td width="133">• Confirm digestion of pSB1k3 by
				electrophoresis, then purification</td>
				<td width="113">• Test Tm of YFP<br />
				• ligation: 22M+10I, 13K+10I</td>
				<td width="114">• Tm of YFP is 54 degree • transform the
				ligation results.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.17th Sunday</td>
		<td>
		<table width="620" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>• PCR 22M<br />
				• purify Vgb, RFP, RFP-tetR, YFP-tetR. Gibson PCR.</td>
				<td>• ligation the purified the fragments in yesterday.</td>
				<td>• 22M PCR<br />
				• Transform the ligation results.</td>
			</tr>
		</table>
		</td>
	</tr>

</table>

<p>&nbsp;</p>
<h1>Week3</h1>
<table id="notesheet" width="713" border="1" cellspacing="0"
	cellpadding="1">
	<tr>
		<td width="87"><strong>Day</strong></td>
		<td width="616"><strong>Note</strong></td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.18th Monday</td>
		<td>
		<table id="intable" width="541" border="0" cellspacing="0"
			cellpadding="1">

			<td width="128">• Genome extraction of E.coli</td>


			<td width="196">• PCR of NirB<br />
			• cut 10I with X+P, cut 22M, 13K with E+S, cut pSB1k3 with E+P</td>
			<td>• Ligate: 10I+13K, 10I+22M <br />
			• Repeat NirB PCR</td>
			<td>
			<p align="left">• Culture 11P<br />
			• Miniprep 10I, 22M, 13K</p>
			</td>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul 19th Tuesday</td>
		<td>
		<table id="intable" width="615" border="0" cellspacing="0"
			cellpadding="1">

			<td width="140">• mini-prep: 10I+13K, 10I+22M</td>


			<td width="213">•insert 10I+13K, 10I+22M into pSB1k3</td>
			<td width="110">•transform: 5E, 3C, 7C, 1K, 1I from the
			distribution plate</td>
			<td width="144">•transform 10I+22M, 10I+13K</td>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.20th Wednesday</td>
		<td>
		<table width="610" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="170">•Colonies of 22M+10I, 13K+10I, 5E, 3C, 7C, 1K,
				1I confirmed</td>
				<td width="102">• Gibson PCR</td>
				<td width="250">•Colony PCR 22M+10I, 13K+10I, 5E, 3C, 7C, 1K,
				1I</td>
				<td width="80">•PCR NirB</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.21th Thursday</td>
		<td>
		<table width="618" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>•PCR verification of 22M+10I, 13K+10I, 5E, 3C, 7C, 1K, 1I
				</td>
				<td>• Gibson PCR • Run the results of PCR verification. Bands
				confirmed.</td>
				<td>• Culture the 22M+10I, 13K+10I, 5E, 3C, 7C, 1K, 1I •
				Purification of Gibson PCR results</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.22th Friday</td>
		<td>
		<table width="618" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="117">• PCR amplification of Gibson assembly results
				</td>
				<td width="144">• Mini prep: 22M+10I, 22.Presever in -20<br />
				• Medi prep: 1K,1I,3C,5E,7C<br />
				• Gibson Assembly fail.</td>
				<td width="164">• PCR NirB by Phusion<br />
				•Repeat PCR by changing Pnibr to Gnirbr<br />
				•Cut the mini and medi prep results with E</td>
				<td width="185">•Run the results of PCR and digestion. Fail in
				PCR of NirB, succeed in 10I+3K and 10I+22M ligation.</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.23th Saturday</td>
		<td>
		<table width="613" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="237">•Double digestion of 13K+10I, 22M+10I, pSB1c3

				</td>
				<td width="169">• Fail in purification of Medi prep</td>
				<td width="201">• PCR NirB<br />
				• Ligate NirB+13K+10I, Vgb+22M+10I</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.24th Sunday</td>
		<td>
		<table width="608" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="244">• Gibson assembly: NirB+RFP+tetR<br />
				• Cut results of Gibson assembly and pSB1c3.</td>
				<td width="164">• Purify the ligation results in yesterday</td>
				<td width="194">• ligate with backbone • Culture 1I, 1K, 3C,
				5E, 7C, 11P</td>
			</tr>
		</table>
		</td>
	</tr>

</table>
<p>&nbsp;</p>
<h1>Week4</h1>
<table id="notesheet" width="691" border="1" cellspacing="0"
	cellpadding="1">
	<tr>
		<td width="63"><strong>Day</strong></td>
		<td width="630"><strong>Note</strong></td>
	</tr>

	<tr>
		<td id="sheetleft">Jul.25th Monday</td>
		<td>
		<table id="intable" width="541" border="0" cellspacing="0"
			cellpadding="1">

			<td width="128">• Transform Pnirb+13k+10I+pSBK3-2</td>


			<td>• Place the culture in 4 degree</td>
			<td>• Medi-and mini-prep of five cultre</td>
			<td>•Gibson Assembly confirmation by gel</td>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul. 26th Tuesday</td>
		<td>
		<table id="intable" width="610" border="0" cellspacing="0"
			cellpadding="1">

			<td width="134">• Cut Pnirb, Pvgb,(E+S)<br />
			• Cut 10I+13K, 10I+22M.(X+P)</td>


			<td width="167">• Ligation: vgb+10I+22M, nirB+10I+13K,</td>
			<td width="172">• Ligation: pSBK13+vgb+10I+22M,
			pSBK13+nirB+10I+13K</td>
			<td width="129">• Transform the ligation results.</td>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.27th Wednesday</td>
		<td>
		<table width="608" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="170">• No colony on the plate<br />
				• Gibson assembly</td>
				<td width="184">• Run the results of Gibson assembly</td>
				<td width="248">• Excise the bands, the purify the DNA<br />
				• Gibson Assenmly</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.28th Thursday</td>
		<td>
		<table width="609" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="607">•2011 China Meet-up @ Hefei</td>

			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.29th Friday</td>
		<td>
		<table width="607" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td>•2011 China Meet-up @ Hefei</td>
			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.30th Saturday</td>
		<td>
		<table width="620" border="0" cellspacing="0" cellpadding="1">
			<tr>


			</tr>
		</table>
		</td>
	</tr>
	<tr>
		<td id="sheetleft">Jul.31th Sunday</td>
		<td>
		<table width="600" border="0" cellspacing="0" cellpadding="1">
			<tr>
				<td width="368">• Culture 22M+10I, 13K+10I</td>
				<td width="228">• Cut a0H, 20J, 22B</td>

			</tr>
		</table>
		</td>
	</tr>

</table>
<br />
<br />
</div>
<!--page1-->
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1>Data/Protocol</h1>
</div>
</div>
</div>
<div id="framecontent">
<h1>Jul.13th Wednesday</h1>

<p><strong>Systems of restriction digestion with EcoRI and
PstI</strong></p>
<p>
<table style="margin: 15px;" width="110" height="200" border="1"
	cellspacing="0" cellpadding="1">
	<tr>
		<td>Plasmid</td>
		<td>1μL (>100ng)</td>
	</tr>
	<tr>
		<td>EcoRI</td>
		<td>1μL</td>
	</tr>
	<tr>
		<td>PstI</td>
		<td>1μL</td>
	</tr>
	<tr>
		<td>10×Buffer Tango</td>
		<td>2μL</td>
	</tr>
	<tr>
		<td>ddH2O</td>
		<td>15μL</td>
	</tr>
</table>
<img src="http://2011.igem.org/wiki/images/c/c3/0713program.png"
	width="200" height="200" /></p>
<p><strong>Temperature grad</strong><br />
56℃,57.4℃,60.2℃,62.9℃,64.3℃,65.8℃</p>
<div id="framecontent">
<p>&nbsp;</p>

<p><strong>PCR system (test the Tm of the primers
CP1&amp;CS, NP&amp;NS)</strong></p>

<table style="margin: 15px;" width="110" border="1" cellspacing="0"
	cellpadding="1">
	<tr>
		<td>10×Buffer</td>
		<td>2μL</td>
	</tr>
	<tr>
		<td>dNTPs</td>
		<td>0.5μL</td>
	</tr>
	<tr>
		<td>primers CP1 (NP)</td>
		<td>1μL</td>
	</tr>
	<tr>
		<td>primers CS (NS)</td>
		<td>1μL</td>
	</tr>
	<tr>
		<td>Template</td>
		<td>1μL</td>
	</tr>
	<tr>
		<td>rTaq</td>
		<td>0.2μL</td>
	</tr>
	<tr>
		<td>H2O</td>
		<td>14.5μL</td>
	</tr>
	<tr>
		<td>Total</td>
		<td>20μL</td>
	</tr>
</table>
</p>
<p>Within each compartment are<strong> components</strong>: include
different types of biomass ,substrates , products. biomass is often
divided into active microbial species, inert cells, and extracellular
polymeric substances(EPS).</p>
<p>The components can undergo transformation, transport, and
transfer <strong>processes</strong>. For example, substrate is consumed,
and this leads to the synthesis of new active biomass.</p>
<p>All process affecting each component in each compartment are
mathematically linked together into a<strong> mass balance
equation</strong> that contains rate terms and parameters for each process.</p>
<p><strong>Model Selection:</strong>Many kinds of Mathematics models
have been founded to describe a system of biofilm. Models of different
dimensions (1d, 2d, 3d) focus on different properties of a biofilm.
Since we care most about the oxygen concentration gradients
perpendicular to the substratum, <strong>numerical
1-dimensional dynamic model(N1)</strong> would be a proper choice for us.</p>
</div>
<!--bgcolors--></div>
<!--important--></div>
<!--importantcontainer-->
<p style="clear: both;"></p>
<div id="page2">
<div class="block" id="nsheet"><img
	src="http://ung.igem.org/wiki/images/4/42/Biofilmcomp.png" width="640"
	height="464" style="margin: 5px;" />
<p>&nbsp;</p>
</div>
<div class="block" id="nsheet">
<h1>Early July</h1>
<p>Pre-experiments with biofilm formation with circular and non
circular silicone tube, 24 well plate on different support including
glass, paper, plastic film, rubber. The final material are used based on
the easiness biofilm form on them and on the easiness to observe under
microscope.</p>
<img
	src="http://2011.igem.org/wiki/images/b/be/20110711-3nP4100X0877.jpg"
	width="400" style="margin-left: 20px;">
<p>&nbsp;</p></div>
<div class="block" id="nsheet">
<h1>28th July</h1>
<p>13.30: DH5ɑ 11p 5mlX4<br />
23.00: silicone tube set at 37℃</p>
</div>
<div class="block" id="nsheet">
<h1>29th July</h1>
<p>13.00: LB culture 50ml with circular culture medium. LB culture
50ml with noncircular culture medium.</p>

</div>
<div class="block" id="nsheet">
<h1>31st July</h1>
<p>13.00: -80℃ storing silicone tube. A thick white and loosely bond
substance is seen on the inner wall of the 5mm silicone tube, and on the
inner wall of the 1mm silicone tube a flatter and smoother white
substance. Especially obvious where the tube turns. Possibly because the
speed of culture flow is slower.</p>

</div>
</div>
<!--page2--> <script type="text/javascript"> 
document.getElementById('bb').onclick= function(){
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 document.getElementById('page1').style.display='block'}
 
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</div>
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<div style="display: none" class="frame" id="rightnav">
<div class="bgcolors" id="round">
<p><a name="jumptop" id="bb">&nbsp; Biobrick Group&nbsp;</a>|<a
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</div>
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</html>
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        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